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June 4, 2020 Comments Off on AiiDA Virtual Tutorial July 2020

The AiiDA team is pleased to announce details for our annual tutorial week!

Description

Due to the ongoing safety concerns related to the COVID-19 pandemic, the introductory tutorial to AiiDA from the 7th to the 10th of July 2020, originally planned to take place in Vilnius, will now be organised in a virtual format.

The goal of this 4 day-tutorial is to help students and researchers from the field of computational materials science get started with writing reproducible workflows. They will be introduced by experts in the field (including the developers of the code) to the use of AiiDA, a state-of-the-art framework for provenance tracking and workflow management designed to support high-throughput research, and will gain in-depth hands-on experience using a tool that they can directly apply to their own research. Participation both from academia and from industry is encouraged.

The AiiDA framework is a tool for workflow management and provenance tracking, which is backed by a significant community of users and developers, and has interfaces to more than 30 materials science codes (see plugin registry), including (among others) to the ab initio codes Quantum ESPRESSO, VASP, cp2k, Castep, Siesta, Fleur, Crystal, NWChem, Wannier90, and Yambo. AiiDA’s permissive open source license (MIT) enables participants to use it both in academic and commercial settings. By virtue of its general design and flexible plugin system, AiiDA is easily extended to new codes and new use cases.

Talks will be pre-recorded and made available to participants before the event, and hands-on tutorials will be held viaZoom. In order to avoid losing time on installation issues, participants will have the option to connect to virtual machines preconfigured with AiiDA (or to come with AiiDA already installed on their laptop via the Quantum Mobile virtual machine).

The event will mostly focus on in-depth tutorials on using AiiDA and on writing workflows. It will also include some talks on how AiiDA has been already used in production, given by the organisers and the core developers of AiiDA; on advanced aspects of workflow management; on designing and writing new AiiDA plugins; and on research data management (RDM) and how to write data management plans (DMPs), especially when using AiiDA and the Materials Cloud.

Key Details

When: From July 7th, 2020 to July 10th, 2020.Where: Virtual Zoom MeetingsRegistration: Fill this online form.Registration deadline: June 19th, 2020. After the deadline, we will select participants if there are more applications than the number of available spaces. Confirmation of acceptance will be sent to applicants at the latest on June 26th, 2020.

Participation to the event is free of charge. Up to 80 participants will be chosen (split into two time-zone groups), in order ensure the possibility for the AiiDA-core developers and tutors to provide direct feedback to all participants during the hands-on sessions.

Speakers & organisers

Tutorial lectures and assistance during hands-on session will be provided by the organisers and a team of core AiiDA developers: Sebastiaan Huber, Leopold Talirz, Yakutovich Aliaksandr, Casper Andersen and Francisco Ramirez.

For general information concerning the tutorial you can contact Chris (christopher.sewell@epfl.ch) or Marnik (marnik.bercx@epfl.ch).

Tentative schedule

Below is a tentative schedule for the event (click to zoom). Two time slots will be provided for each session to accommodate for participants in different timezones. Times may be subject to change, based on the final selection of participants.

Funding

We are very grateful to our sponsors for helping to make this event possible:

Coordinates

Schedule

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About

The Coding Week is an annual event meant to develop, discuss, and focus on the core of AiiDA, i.e., the aiida-core package.

Core developers, mainly from EPFL, but also external, are invited for a week of focused development in a scenic and social setting.
The week includes a group excursion. Last year this was a walk/trek in the surrounding Alps with snowshoes, and a memorable view at the local Aletsch glacier.

Since the recent release of AiiDA 1.0.0, we are looking forward to 1.1.0. Several subjects have already been circulated internally to focus on and will be discussed in plenum in Fiesch.

Funding

Out of the 30 people invited, 16 will be participating. By default, participants are expected to cover their costs for travel and lodging, but we aim to reimburse the cost of lodging for participants who require financial assistance.

We are very grateful to our sponsors for helping to make this event possible:

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April 22, 2019 Comments Off on AiiDA project & Google Season of Docs

The AiiDA project is happy to announce its application to participate in this year’s Google Season of Docs (GSoD). GSoD tries to bring open source projects and technical writers together: To give technical writers experience in contributing to open source projects and help opens source projects to improve their documentation and interact with the technical writing community.

What happens next

May 29, 2019 Start of technical writer application period. More details about the application process can be found in the technical writer guide, where also the application form will be published

June 28, 2019 End of technical writer application period

Prospective technical writers

Are you a technical writer with a background in (or affinity to) computational materials science, physics or chemistry? Would you be interested in boosting a tool that lets researchers manage thousands of simultaneous calculations on supercomputers and helps them work in an open-science environment, making their research reproducible and FAIR? Then please read on!

If you would like to discuss your application or project ideas, please feel free to contact Kevin or any of the other coordinators and prospective mentors:

Computational materials science involves screening thousands to hundreds of thousands of materials for key figures of merit. Running thousands of calculations is a nontrivial task in itself and calls for an infrastructure to help orchestrate the calculations and organize the output data, while also ensuring that others can easily reproduce the work. To this aim, there are two important requirements for such an infrastructure: First, it must be flexible enough to support a large variety of simulation workflows; second, it should require minimal overhead compared to the ‘conventional’ way of running simulations.

AiiDA is a python package that is built to make this possible: while automating simulations on supercomputers, it stores the full provenance of data and calculations in a directed graph (see Figure 1c) that can be easily queried using a high-level interface. Moreover, it provides a workflow engine that make it possible to automate and run complex simulations with simple, small snippets of code by using predefined ‘turn-key’ workflows (see Figure 1). Currently, 34 plugins provide support different codes and provide over 50 workflows to compute basic and advanced materials properties.

Following several alpha and beta versions, 2019 will see the release of AiiDA version 1.0. AiiDA 1.0 brings a number of new features, a redesign of the provenance model as well as of many AiiDA internals. The projects for the 2019 GSoD will focus on updating the available documentation and tutorial material to reflect the changes which were introduced in AiiDA 1.0.

Note: These are project ideas. We highly welcome your suggestions on how to make the documentation more effective as well as how to best accommodate your talents as a technical writer.

Moreover, from the perspective of a new user, it would be probably easier to find all existing tutorials in a consistent and updated form in one place (e.g. a with tag with the versions on which the tutorials were tested, see also http://matgenb.materialsvirtuallab.org/). On top of that, several codes that AiIDA supports are not represented with a tutorial — it would be great to add new jupyter notebooks, ideally on MyBinder, showcasing how to use AiiDA with those plugins.
We can suggest plugins which are well developed and contain advanced features (and for which we know the authors) and can help the technical writers in prioritizing.
The technical writer could then test examples from the plugin repositories and create a tutorial, maybe even in form of a screencast (some videos can already be found on the Materials Cloud), explaining a common workflow using AiiDA and one of the many AiiDA plugins.
Existing videos and screencasts could be updated, or at least annotated, to reflect the changes with the new major release. An ambitious technical writer might even set out to develop a online course teaching the basics of AiiDA (writing workflows, querying the database) in the form of a MOOC. An bit less ambitious goal would be to bring existing tutorials on our youtube channel into a consistent format.

AiiDA docs

The AiiDA documentation, written in Sphinx and hosted on ReadTheDocs, is our main effort to document the usage and development of AiiDA. A technical writer could contribute in several ways to this documentation: First, the complete documentation needs to be checked for compatibility with the AiiDA 1.0 release. Second, the documentation can still be extended and refactored to improve the user experience. Sometimes, we encounter issues that are not documented or are not clear enough, or we realise that the organisation of the documentation does not make it easy to find the section that is being searched for. Hence, it would be great to check for frequent issues on the mailing list and include those in the documentation.

AiiDA web site

We feel that our web page could to be updated to better highlight the main features of AiiDA. Currently, the feature section is hidden and should be updated to reflect the feature set of the most recent release. A technical writer could help developing this section and writing a ‘why use AiiDA’ section, ideally supported by appealing visualizations.
We would welcome interactive feature demonstrations or a carousel with examples in which AiiDA was used. This could include links to the databases on the Materials Cloud archive or even interviews with researchers, discussing how they used AiiDA in their research and publication process.

Schedule

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Talks marked by (R) are planned to be recorded

About

This 3.5-day tutorial is designed to get Master students, PhD students and Postdocs from the field of computational materials science started with writing reproducible workflows. Participants will be introduced to the state of the art in workflow management and high-throughput computations by experts in the field, and gain in-depth hands-on experience using a tool that they can directly apply to their own research.

Our tool of choice is the AiiDA framework for workflow management and provenance tracking, which is backed by a significant community of users and developers, and has interfaces to more than 20 materials science codes (see plugin registry), including to the ab initio codes Quantum ESPRESSO, VASP, cp2k, Castep, Siesta, Fleur, Crystal, NWChem, Wannier90, and Yambo. AiiDA’s permissive open source license (MIT) enables participants to use it both in academic and commercial settings. By virtue of its general design and flexible plugin system, AiiDA is easily extended to new codes and new use cases.

The first day will serve as an introduction to AiiDA 1.0. In order to avoid losing time on installation issues, all participants will have the option to connect to a personal virtual machine preconfigured with AiiDA (or to come with AiiDA 1.0 already installed on their laptop).

The second day will cover workflows in AiiDA 1.0. Following input from the workshop questionnaire, participants will first learn the concepts using aiida-quantumespresso, and then have the option to get to know other plugins (such as aiida-vasp) in the following days.

In the remaining 1.5 days, participants will be able to start working on their own projects, choosing among three topics:

Throughout the tutorial, lectures by the organizers and core developers of AiiDA are complemented by talks by the invited speakers highlighting the use of the workflows in computational materials science.

Discussion sessions, as well as a poster session (NEWPoster abstracts) and an open-mic session are scheduled to foster interaction between the participants, to discuss and answer questions.

While this tutorial is deliberately open to computational materials scientists at many levels, we do require the following for participation:

familiarity with a Unix operating system and the bash shell (or equivalent)

familiarity with python

familiarity with a job scheduler (e.g. slurm, torque, sge, …)

full participation for (at least) the last 2.5 days

Speakers & organisers

The tutorial is organised by Leopold Talirz (EPFL, CH), Sebastiaan Huber (EPFL, CH), Espen Flage-Larsen (SINTEF, NO), Alberto García (ICMAB, ES) and Andrea Ferretti (CNR, IT) who bring expertise in a diverse set of ab initio codes and their applications in different work environments (universities, research institutes and companies).

The following invited speakers will illustrate the use workflows in their research using a recent example, highlighting both the challenges encountered and possible solutions.

Stefaan Cottenier (UGent, BE)

Marco Govoni (ANL, US)

Fawzi Mohamed (FHI, GE)

Guido Petretto (UC Louvain, BE)

Tutorial lectures and assistance during hands-on session will be provided by a team of core AiiDA developers and active plugin developers:

How to get there

Funding

The tutorial will be offered free of charge, with roughly 40 participants. By default, participants are expected to cover their costs for travel and lodging, but we aim to reimburse the cost of lodging for participants who require financial assistance (which they need to motivate during registration).

We are very grateful to our sponsors for helping to make this event possible:

An AiiDA plugin migration workshop will be held at EPFL Lausanne, Switzerland, aiming at collecting about 20 participants.

The workshop will start on Monday 25th March at 2PM and end on Friday 29th March at 1PM.

We are in the process of preparing the AiiDA code towards the 1.0 release, in which we have recently introduced python 2 + python 3 support (already available in the 1.0 alpha releases). While we strive to always maintain back-compatibility, we have realised that there were a few needed improvements to the API and we felt that the 1.0 release was the right moment to introduce them. (Note: while existing “codebases” will need (often very straightforward) migration-which is
what this workshop is for-existing “databases” will be fully compatible and be automatically migrated when users upgrade to AiiDA 1.0).

The aim of this workshop is to directly support AiiDA plugin developers in the migration of their plugins to support both python 2 and python 3, as well as the changes introduced in AiiDA 1.0.

This workshop is focused on migrating existing plugins (a full list of the plugins supporting almost 60 different codes can be found on the AiiDA plugin registry page). Another tutorial for new developers of plugins and workflows will be held in Lausanne in the week 20-24 May 2019 and will be advertised soon (stay tuned!).

We will also reserve some time for discussions on plugin interfaces and their homogenisation and common APIs, exploiting this unique occasion bringing together many plugin developers.

Main topics

explanation of the changes on 1.0;

hands-on workshop on porting plugins to py2+3 and new aiida 1.0;

discussions on common interfaces to different plugins for common functionalities (e.g. crystal structure relaxation, band structure, …);

discussion of automated plugin testing against different versions of AiiDA, python, …

Program
Every day there will be an informal coffee break from 11:00 – 11:15 and 16:00 – 16:15

On the first day, an introductory talk was delivered by Spyros Zoupanos about the general architecture and design of AiiDA, after which the participants started with the hands-on exercises to get to know with AiiDA’s interface.
A more detailed presentation on the workflow system was given by Martin Uhrin.

Introduction by the organisers of the AiiDA tutorial (May 2018)

On the second and third day, Giovanni Pizzi and Leonid Kahle gave an exposé on their research projects that actually implemented and used the AiiDA platform to discover new two-dimensional materials and solid state ionic conductors in a high-throughput way, respectively.
This gave a good idea to the tutorial participants of the potential of AiiDA in a broader sense.

Room with participants at the AiiDA tutorial

The opportunity was also used to introduce participants to the concept of open source collaboration – in particular, Sebastiaan Huber gave a crash course on the use of Git and GitHub to contribute to open source projects (branches, forks and pull requests).

During the tutorial, a poster session was also organized, where the participants had the chance to present their own work and get to know that of their colleagues, in an informal setting with drinks and fingerfood.

Poster session at the AiiDA tutorial

In between these extra events, the main focus lay on introducing the participants to AiiDA through a hands-on tutorial and exercises, with all the instructors available to provide support and explanation in person.
The participants were very committed during the tutorial and already provided comments to improve the tutorial during the event.

Instructors helping out participants at the tutorial

At the end of the tutorial, all participants were asked to give feedback by completing an evaluation questionnaire, which will be used to further improve the tutorial and AiiDA itself.
The feedback was overall very positive, with the tutorial graded with an average vote of 9.0 out of 10, and all votes between 8 and 10.
All participants stated that the well-prepared and helpful instructors helped the participants to get really well acquainted with AiiDA and that it may very well help them with their own work and research.
The scientific talks that gave examples of AiiDA in real-world scientific projects were also well received as they gave a more intuitive example of the power and potential of AiiDA.

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January 27, 2017 Comments Off on Report on AiiDA tutorial: 24-25 January 2017 at ICTP in Trieste, Italy.

The end of January of 2017 saw the eighth hands-on tutorial for AiiDA within the “Advanced Workshop on High-Performance & High-Throughput Materials Simulations using Quantum ESPRESSO” organised at and by ICTP in Trieste. The tutorial was kicked off by an introductory lecture by Giovanni Pizzi (EPFL), explaining the philosophy and architecture behind AiiDA, and how the ADES model facilitates and simplifies performing and sharing calculations, under the umbrella of complete data provenance. After the scene was set, the approximately 75 participants went to their workstations to start with the first of the hands-on sessions. A completely configured virtual machine was provided for each individual participant, to which they only had to login and they were on their way. The first session served to familiarize the users with Verdi, a command line interface which acts as the user’s tool to interact with AiiDA. With the tools in hand to put AiiDA to good use, the participants learned by example how a Quantum Espresso calculation can be easily launched as AiiDA takes care of a lot of the repetitive work behind the scenes.

The virtual environment in which the participants were working came with a database filled with pre-computed calculations, which allowed the aptitude of AiiDA in working with big data sets to be displayed effortlessly. The QueryBuilder, the tool provided by AiiDA to efficiently query a user’s collection of calculations, was introduced and a step-by-step tutorial showed the participants how it could be used to efficiently analyze a large collection of calculations on perovskites. The final session detailed how the users could easily create such a big collection of calculations themselves, in a high-throughput manner, through the concept of Workflows.

Throughout the tutorial, five members of the AiiDA team were present to answer any questions of the participants and give introductory talks at the beginning of a new hands-on session. After the hands-on sessions, a good portion of the participants gave their feedback on the quality of the tutorial and the impact on their skills in using AiiDA. The results are very promising while at the same time they provide the AiiDA team with valuable information on how to improve both the tutorial and AiiDA itself.

The feedback on the quality of the tutorial itself, in terms of content and planning, were overall very positive

Participant feedback on the quality of the tutorial

The results of the feedback also show that the tutorial really helped improve the skill and knowledge of the participants regarding the use of AiiDA

The skill level of the participants before and after the tutorial

The AiiDA team thanks the organisers of the event for making this tutorial possible and all the participants for their enthusiasm. Until the next AiiDA event!

👤admin🕔
December 13, 2016 Comments Off on Report from the AiiDA coding week – Dec 2016

Last week (5-9 Dec 2016) we had a coding week for AiiDA, to which 15 people participated (roughly half of them core developers from the AiiDA, and the other half were developers who were interested in contributing to the platform).

The coding week has taken place in Leysin, in the Swiss Alps. A few discussion or work topics had been identified before the start by the AiiDA team, and have been addressed during the week. In particular, the following topics have been discussed and the result has been summarised in a draft document for later implementation:

New more efficient implementation of the AiiDA daemon

How third-parties can contribute to Materials Cloud sections

Redesign of the ORM classes (in particular Node) to improve the way multiple backends are supported

A few discussions have also led to new branches of development, that will be soon merged into the develop branch (and appear in a future release):

AiiDA plugin interface integrated with pip

Various improvements and bug fixes to the SQLAlchemy backend implementation

Finally, the remaining work topics have been taking up a large part of the coding sessions, and most of the code has already been merged into the develop branch:

Redesign of the AiiDA documentation, with a more clear structure, removal of duplicates, a new and more clear installation section.

Simplified procedure to install AiiDA.

New testing infrastructure to test in parallel any database backend (currently, both Django and SQLAlchemy)

Removal of the DbPath (transitive closure) table and triggers, and replacement with a dynamically created query (using either PostgreSQL recursive queries or PostgreSQL functions). The performance of these queries has been optimised.

Beside programming, most participants have taken place to an outdoor hiking activity on Wednesday morning to Berneuse, close to Tour d’Aï, that was a great team building opportunity. Participants have also enjoyed after-dinner sessions with board and card games.

The outcome of the feedback, summarised below, has been very positive, both in terms of participation, organisation, and improvement to the code. The results indicate also that similar events should be organised again in the future, with a frequency of about twice a year.